2I87

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EHIPDB code 1EHI

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1242.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.661α = 90
b = 66.408β = 96.24
c = 78.59γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2001-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
127999.70.03826.93.7468234682337.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.1624.53.83276

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB code 1EHI279.064682344470233699.620.201870.19980.24148RANDOM37.837
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.070.010.27-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.448
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg16.746
r_dihedral_angle_1_deg7.33
r_scangle_it4.256
r_scbond_it3.074
r_angle_refined_deg1.991
r_mcangle_it1.933
r_mcbond_it1.567
r_angle_other_deg1.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.448
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg16.746
r_dihedral_angle_1_deg7.33
r_scangle_it4.256
r_scbond_it3.074
r_angle_refined_deg1.991
r_mcangle_it1.933
r_mcbond_it1.567
r_angle_other_deg1.034
r_mcbond_other0.357
r_symmetry_hbond_refined0.278
r_symmetry_vdw_refined0.248
r_nbd_refined0.23
r_symmetry_vdw_other0.221
r_nbd_other0.206
r_nbtor_refined0.194
r_xyhbond_nbd_refined0.17
r_chiral_restr0.128
r_nbtor_other0.097
r_bond_refined_d0.024
r_xyhbond_nbd_other0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5479
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement